Table 1.
Cytoplasmic CE-interacting proteins identified by LC-MS/MS analysis
Listed are cytoplasmic CE-interacting proteins identified by MS analysis of samples recovered on streptavidin beads after formaldehyde cross-linking of cells expressing bio-cCE or bio-EGFP. The total number of PSMs from three independent experiments is listed. Details of each analysis are in Table S1. For each candidate interacting protein, a cCE enrichment index was calculated as the average of cCE PSMs divided by the average of negative control PSMs plus one. Column six lists proteins that were also identified by BioID, and column seven identifies proteins that appear in the integrated Human RNA-Binding Proteome (17). Proteins in boldface type were validated by Western blotting (Fig. 2). NA, not applicable.
| Gene symbol | Gene name | Total PSMs |
cCE enrichment index | BioID | ihRBP | |
|---|---|---|---|---|---|---|
| bio-cCE | bio-EGFP | |||||
| FASN | Fatty acid synthase | 76 | 9 | 6.33 | Yes | Poly(A) |
| KPNB1 | Importin subunit β-1 | 17 | 0 | 5.67 | Poly(A) | |
| EEF2 | Elongation factor 2 | 47 | 6 | 5.22 | Yes | Poly(A) |
| CLTC | Clathrin heavy chain 1 | 40 | 5 | 5.00 | Poly(A) | |
| CCT5 | T-complex protein 1 subunit ϵ | 18 | 1 | 4.50 | Non-poly(A) | |
| CCT7 | T-complex protein 1 subunit η | 20 | 2 | 4.00 | Non-poly(A) | |
| CSE1L | Exportin-2 | 12 | 0 | 4.00 | Non-poly(A) | |
| CCT3 | T-complex protein 1 subunit γ | 24 | 3 | 4.00 | Poly(A) | |
| RUVBL2 | RuvB-like 2 | 11 | 0 | 3.67 | Non-poly(A) | |
| CCT2 | T-complex protein 1 subunit β | 22 | 3 | 3.67 | Non-poly(A) | |
| TUBA3C | Tubulin α-3C/D chain | 35 | 7 | 3.50 | NA | |
| TCP1 | T-complex protein 1 subunit α | 20 | 3 | 3.33 | Poly(A) | |
| TUBB6 | Tubulin β-6 chain | 46 | 11 | 3.29 | NA | |
| CCT8 | T-complex protein 1 subunit θ | 32 | 7 | 3.20 | Yes | Non-poly(A) |
| TUBA1B | Tubulin α-1B chain | 70 | 19 | 3.18 | Yes | NA |
| TUBB | Tubulin β chain | 123 | 37 | 3.08 | Yes | Non-poly(A) |
| TUBB4B | Tubulin β-4B chain | 109 | 33 | 3.03 | Yes | NA |
| PSMD2 | 26S proteasome non-ATPase regulatory subunit 2 | 9 | 0 | 3.00 | Non-poly(A) | |
| CCT6A | T-complex protein 1 subunit ζ | 14 | 2 | 2.80 | Poly(A) | |
| PHGDH | d-3-phosphoglycerate dehydrogenase | 8 | 0 | 2.67 | Non-poly(A) | |
| FSCN1 | Fascin | 8 | 0 | 2.67 | Poly(A) | |
| TIMM50 | Mitochondrial import inner membrane translocase subunit TIM50 | 8 | 0 | 2.67 | NA | |
| AHNAK | Neuroblast differentiation–associated protein AHNAK | 16 | 3 | 2.67 | Yes | Poly(A) |
| HSP90AB1 | Heat shock protein HSP 90-β | 85 | 29 | 2.66 | Yes | Poly(A) |
| HSP90AA1 | Heat shock protein HSP 90-α | 48 | 16 | 2.53 | Yes | Poly(A) |
| FKBP4 | Peptidyl-prolyl cis-trans-isomerase FKBP4 | 10 | 1 | 2.50 | Poly(A) | |
| TLN1 | Talin-1 | 10 | 1 | 2.50 | Non-poly(A) | |
| CCT4 | T-complex protein 1 subunit δ | 22 | 6 | 2.44 | Poly(A) | |
| EIF2S1 | Eukaryotic translation initiation factor 2 subunit 1 | 12 | 2 | 2.40 | Poly(A) | |
| RNH1 | Ribonuclease inhibitor | 7 | 0 | 2.33 | Non-poly(A) | |
| MTHFD1 | C-1-tetrahydrofolate synthase, cytoplasmic | 9 | 1 | 2.25 | Non-Poly(A) | |
| PCBP2 | Poly(rC)-binding protein 2 | 9 | 1 | 2.25 | Poly(A) | |
| HSPA1A | Heat shock 70-kDa protein 1A/1B | 11 | 2 | 2.20 | NA | |
| STIP1 | Stress-induced phosphoprotein 1 | 11 | 2 | 2.20 | Poly(A) | |
| FLNC | Filamin-C | 24 | 8 | 2.18 | NA | |
| TUBA1C | Tubulin α-1C chain | 16 | 5 | 2.00 | Poly(A) | |
| GAPDH | Glyceraldehyde-3-phosphate dehydrogenase | 19 | 7 | 1.90 | Poly(A) | |
| PCBP1 | Poly(rC)-binding protein 1 | 9 | 2 | 1.80 | Poly(A) | |
| ENO1 | α-enolase | 7 | 1 | 1.75 | Yes | Poly(A) |
| KIF5B | Kinesin-1 heavy chain | 5 | 0 | 1.67 | Non-poly(A) | |
| RUVBL1 | RuvB-like 1 | 5 | 0 | 1.67 | Non-poly(A) | |
| FLNA | Filamin-A | 46 | 25 | 1.64 | Poly(A) | |
| RAN | GTP-binding nuclear protein Ran | 6 | 1 | 1.50 | Poly(A) | |
| PFN1 | Profilin-1 | 6 | 1 | 1.50 | Yes | Poly(A) |
| EIF5A | Eukaryotic translation initiation factor 5A-1 | 9 | 3 | 1.50 | Poly(A) | |